Additional file 5 of Deciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profiling: a case study
Bibliographic record
Abstract
Additional file 5 (PDF 11357 KB). Supplementary Fig. 1. UMAP plots showing selected top marker genes for each of the five microglia cell states, including phagocytic AD-associated (a), homeostatic (b), pro-inflammatory CSF1R-RD-associated (c), autophagy CSF1R-RD-associated (d), and peripheral monocyte-derived macrophages (e). Supplementary Fig. 2. CSF1R expression levels in microglia clusters. a UMAPs showing the distribution of CSF1R-RD, healthy, and AD nuclei. b Dot plot and violin plot displaying the gene expression levels of CSF1R in CSF1R-RD, healthy, and AD groups. c UMAP, dot plot and violin plot depicting the gene expression levels of CSF1R in microglia clusters. d Dot plot and UMAP depicting the gene expression levels of TREM2 in microglia clusters. e Dot plot and violin plot showing the gene expression levels of CSF1R in samples. *FDR < 0.05, **FDR < 0.01, ****FDR < 0.0001 (FDR-adjusted p-values using MAST). Supplementary Fig. 3. GPNMB and Iba1 immunohistochemistry in frontal cortex (a–d), anterior cingulate (e–h), and cerebellum (i–l; ml: molecular layer; gl: granular cell layer) in CSF1R-RD. Representative images of frontal cortex from a healthy donor (m,n) demonstrates Iba1+ ramified microglia. Dashed lines indicate borders between gray matter (gm) and while matter (wm). Scale bars: 200 µm (a, c, e, g, i, k, m); 50 µm (b, d, f, h, j, I, n). Supplementary Fig. 4. snRNAseq of astrocyte cell states in CSF1R-RD. a UMAP plots showing the contributions from CSF1R-RD, healthy control, and AD (left), and from each individual sample (right) to the dataset. b UMAP and bar plots showing the four annotated astrocyte states (A0–A3). c Contribution of each astrocyte state per sample. d Contribution of each disease group to each astrocyte state cluster. e Dot plot showing top astrocyte cell state marker genes per cluster (A0: homeostatic; A1–3: reactive). Supplementary Fig. 5. UMAP plots showing selected top marker genes for each of the three oligodendroglia cell states (O1–O3; a–c).
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.993 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".